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[log in to unmask] wrote:
>
>
> Sorry, one other quick question. The canonical HRFs and gamma
> function regressors are built in (it appears) so their
> delays/dispersions cannot be adjusted manually?
You can change these by passing different parameters to spm_hrf.m
These options are not available from the GUI.
I know that you can
> include derivatives with the canonical HRF, but it only gives you two
> derivative functions with built-in delays/dispersions that can't be
> adjusted from what I can see. If you want to customize your own gamma
> functions or canonical HRFs, you need to build them yourself right?
>
Yes. But I would'nt bother for a block design.
Best,
Will.
> Thank you,
>
> Todd Penney
>
>
> Quoting Will Penny <[log in to unmask]>:
>
>> Dear Todd,
>>
>> Nothing really strikes me as unusual.
>>
>> All I can think is - maybe its something to do with the
>> Gamma basis functions, so try the canonical HRF.
>>
>> This will probably make no difference.
>>
>> Did you save a copy of the model specification job file ?
>> If so, perhaps you could mail it to me (not to the list).
>>
>> Otherwise - you could go into Review->Explore Design,
>> plot the design matrix and send the image to me.
>>
>> This may provide some more clues.
>>
>> Best,
>>
>> Will.
>>
>> [log in to unmask] wrote:
>>
>>>
>>>
>>>
>>> Hi Will,
>>>
>>> You are correct - I am doing a 1st level fMRI design as I only have
>>> data from one patient from one session. I am using a 1st order Gamma
>>> function as my model with a window length of 20sec. I fixed the
>>> original problem I was having entering contrasts in the contrast
>>> manager. The fix was available in the SPM archives, which a fellow
>>> from Harvard pointed me to. I am using Windows XP to run SPM5 and
>>> for some reason the command
>>>
>>> feature('JavaFigures',0)
>>>
>>> needs to be run at the MATLAB command prompt to correct the problem
>>> with the contrast manager I was having. Now it will allow me to
>>> enter contrasts properly.
>>>
>>> The contrast vector I am using is [1 0] because I only have two
>>> regressors and I only want to see the effect of the first one.
>>>
>>> ANOVA, as far as I can tell from the SPM5 manual, is used to solve
>>> for the covariates when you ask for a Bayesian analysis of your
>>> model, not when you want the classical method of solving the GLM
>>> applied. Anything that strikes you as incorrect with what I'm doing?
>>>
>>> Thanks
>>>
>>> Todd Penney
>>>
>>> Quoting Will Penny <[log in to unmask]>:
>>>
>>>>
>>>>
>>>> [log in to unmask] wrote:
>>>>
>>>>>
>>>>>
>>>>> Hi Will,
>>>>>
>>>>> I don't see anywhere in SPM5 where you specify ANOVA with or
>>>>> without a constant model.
>>>>
>>>>
>>>>
>>>> SPM5 makes ANOVA models without a constant.
>>>>
>>>> The model functions I am using are Gamma functions if
>>>>
>>>>> that interests you.
>>>>
>>>>
>>>>
>>>> OK. So this is a first level fMRI design.
>>>>
>>>> What is the model and what contrasts are you trying to enter ?
>>>>
>>>> [But you can actually type them in ? - as there was recently a bug
>>>> where you could'nt even do this ...]
>>>>
>>>> Best,
>>>>
>>>> Will.
>>>>
>>>> I don't see anything about ANOVA anywhere though.
>>>>
>>>>> Any thoughts?
>>>>>
>>>>> Thanks for your help.
>>>>>
>>>>> Todd Penney
>>>>>
>>>>>
>>>>> Quoting Will Penny <[log in to unmask]>:
>>>>>
>>>>>> Dear Todd,
>>>>>>
>>>>>> What is the contrast you are trying to enter ?
>>>>>> And what is the model ?
>>>>>>
>>>>>> Some contrasts are invalid.
>>>>>>
>>>>>> For example if you have three conditions and use the ANOVA with
>>>>>> a constant model, SPM will make a design matrix with
>>>>>> 4 columns. The first three for condition effects and the last for
>>>>>> the overall mean.
>>>>>>
>>>>>> The trouble with this model is that it is over-parameterised.
>>>>>> Each column in the design matrix can be gotten from a linear
>>>>>> combination of the other three. So there is
>>>>>> some indeterminacy in the associated regression coefficients.
>>>>>>
>>>>>> The end result is that contrasts like 1 0 0 0
>>>>>> or 0 1 0 0 are not admissable because the associated regression
>>>>>> coefficients are not interpretable.
>>>>>>
>>>>>> But you can look at differences in this model eg 1 -1 0 0
>>>>>>
>>>>>> If you wanted to look at each effect alone you'd use
>>>>>> a different model eg. ANOVA without a constant. Then
>>>>>> there's no problem.
>>>>>>
>>>>>> (Basically, the ANOVA with a constant is a silly model).
>>>>>>
>>>>>> Anyway, what model do you have ?
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Will.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Todd Penney wrote:
>>>>>>
>>>>>>> Hello again all,
>>>>>>>
>>>>>>> I've tried entering the contrasts several different ways, paying
>>>>>>> careful
>>>>>>> attention not to exceed the number of valid contrasts based on
>>>>>>> the number of
>>>>>>> conditions I have. This problem is still persisting. I'm
>>>>>>> beginning to think
>>>>>>> there is some problem with the way SPM5 is set up on my PC. Any
>>>>>>> suggestions
>>>>>>> from SPM experts?
>>>>>>>
>>>>>>> Thank you
>>>>>>>
>>>>>>> Todd Penney
>>>>>>> University of Alberta
>>>>>>>
>>>>>>> ----- Forwarded message from [log in to unmask] -----
>>>>>>> Date: Wed, 15 Feb 2006 11:55:36 -0700
>>>>>>> From: [log in to unmask]
>>>>>>> Reply-To: [log in to unmask]
>>>>>>> Subject: problems setting up contrasts using SPM5
>>>>>>> To: [log in to unmask]
>>>>>>>
>>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> I'm at the step of setting up contrasts to review my results
>>>>>>> using SPM5. In
>>>>>>> the contrast manager when I attempt to put in a contrast vector I
>>>>>>> get an error
>>>>>>> saying "No valid contrast vector defined". I've tried every way
>>>>>>> of putting in
>>>>>>> the vector using quotes, brackets, commas between elements, etc.
>>>>>>> However
>>>>>>> nothing seems to work. The contrast is named also, so there is
>>>>>>> no problem with
>>>>>>> that. Has anyone had a similar problem?
>>>>>>>
>>>>>>> Thank you
>>>>>>>
>>>>>>> Todd Penney
>>>>>>> University of Alberta
>>>>>>> Edmonton, Alberta, Canada
>>>>>>>
>>>>>>> ----- End forwarded message -----
>>>>>>>
>>>>>>>
>>>>>>> ----- End forwarded message -----
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> William D. Penny
>>>>>> Wellcome Department of Imaging Neuroscience
>>>>>> University College London
>>>>>> 12 Queen Square
>>>>>> London WC1N 3BG
>>>>>>
>>>>>> Tel: 020 7833 7475
>>>>>> FAX: 020 7813 1420
>>>>>> Email: [log in to unmask]
>>>>>> URL: http://www.fil.ion.ucl.ac.uk/~wpenny/
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>> --
>>>> William D. Penny
>>>> Wellcome Department of Imaging Neuroscience
>>>> University College London
>>>> 12 Queen Square
>>>> London WC1N 3BG
>>>>
>>>> Tel: 020 7833 7475
>>>> FAX: 020 7813 1420
>>>> Email: [log in to unmask]
>>>> URL: http://www.fil.ion.ucl.ac.uk/~wpenny/
>>>>
>>>>
>>>
>>>
>>>
>>>
>>
>> --
>> William D. Penny
>> Wellcome Department of Imaging Neuroscience
>> University College London
>> 12 Queen Square
>> London WC1N 3BG
>>
>> Tel: 020 7833 7475
>> FAX: 020 7813 1420
>> Email: [log in to unmask]
>> URL: http://www.fil.ion.ucl.ac.uk/~wpenny/
>>
>>
>
>
>
>
--
William D. Penny
Wellcome Department of Imaging Neuroscience
University College London
12 Queen Square
London WC1N 3BG
Tel: 020 7833 7475
FAX: 020 7813 1420
Email: [log in to unmask]
URL: http://www.fil.ion.ucl.ac.uk/~wpenny/
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